Cultivar-Specific Rhizosphere Microbiome Functional Gene Associations with Soil Nutrient Availability and Yield in Selected Hybrid and Conventional Rice Varieties
Year: 2026
Type: article
Abstract: Hybrid rice outyields conventional rice, but the role of rhizosphere microbiome in this yield advantage remains unclear. We conducted a single-site field experiment to compare three hybrid rice cultivars with one conventional variety. We tested whether the hybrid rice cultivars were associated with distinct rhizosphere microbial consortia, and whether these consortia correlated with soil nutrient availability and yield. Our results showed that the hybrid cultivars produced significantly higher yields than the conventional variety. Rhizosphere soil was collected at booting and mature stages. We integrated 16S rRNA and metagenomic sequencing, soil physicochemical and enzyme activity analyses, and structural equation modeling to explore associations among rice genotype, microbial community, nutrient availability, and yield. Hybrid rice showed higher yield and 1000-grain weight (Yongyou-1540: 69.76 g/plant, 26.85 g). Genotype-associated differences in microbiome were strongest at booting: hybrids enriched Pseudomonadota and Chloroflexota but depleted Acidobacteriota; genera Geobacter, Anaeromyxobacter, and Burkholderiaceae were enriched. Hybrid rhizospheres had higher available phosphorus and potassium (Heliangyou-165: +62.8% P and +24.7% K at booting; +18.4% P and +350.8% K at maturity). Metagenomic profiling revealed a higher abundance of genes associated with nitrogen fixation, siderophore biosynthesis, and sulfur cycling pathways. Nitrogen fixation gene abundance correlated with alkali-hydrolyzable N (r = 0.66), siderophore biosynthesis with available P (r = 0.73), and sulfate respiration with available K (r = 0.61). Enzyme activities showed genotype-and stage-dependent patterns. Structural equation modeling supported a sequential association path: genotype → microbial community (β = 0.58) → soil nutrient composite (β = 0.52) → grain yield (β = 0.44). The indirect effect of genotype on yield via microbiome and nutrients was significant (β = 0.13), while the direct effect was not. The yield advantage observed in the tested hybrid cultivars was accompanied by cultivar-associated differences in rhizosphere microbiomes that correlate with enhanced nutrient bioavailability during critical growth stages. These correlative findings suggest a potential belowground ecological pathway linking cultivar identity, rhizosphere microbiome functional potential, nutrient availability, and yield; however, they do not demonstrate a causal role of the microbiome in the yield advantage of hybrid rice. Given the single-site, single-year design and the use of only one conventional control cultivar, these results should be considered preliminary and require validation across broader genotype panels and environments. Experimental validation is required to test the hypothesized microbial associations.
Source: Agronomy
Authors: Shufen Zhou, Bo Ling, Zhongchun Chen, Jianmin Chen
Institution: Fujian Academy of Agricultural Sciences
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,137
OpenAlex ID: W7212053112